Ensembl Anopheles What's New v27.2c.1 (14 December 2004)

	Ensembl: Latest Developments
	v27.2c.1 Update This release includes a lot of new and updated data including the addition of the dog genome, LD data for human, a patched human gene set, new imports of fly and worm, and updated SNP sets for a number of species. Also new for this release is the variation database, which entirely replaces the SNP and Lite databases. This database is an entirely new schema to store SNPs and other genomic variations, plus genotype, population, and LD data. The Ensembl website has moved to new hardware for this release, and as a result the site is quicker to respond and can more easily cope with the increased traffic we are receiving. We hope you like the improvement. New data in v27  Caenorhabditis briggsae From release 27, C. briggsae will no longer be included in Ensembl. This genome is available from the WormBase database and browser: http://www.wormbase.org/db/seq/gbrowse/briggsae.  Comparative genomics (ensembl_compara_27_1)   New orthologues build   New load of chimp direct mapped orthologues   No human paralogues for this release   New family build   D. melanogaster - against Anopheles TRANSLATED_BLAT - against Bee TRANSLATED_BLAT   C. familiaris - against Human BLASTZ_NET (UCSC)/BLASTZ_NET_TIGHT(in-house) - against Fugu TRANSLATED_BLAT - against Tetraodon TRANSLATED_BLAT - against Danio TRANSLATED_BLAT - against Chicken TRANSLATED_BLAT - synteny against human   Fixed score and %identity in all BLASTZ_NET alignments involving human chromosome Y  Mart database (ensembl_mart_27_1)   New build  Core database   Tandem Reapeat Feature (TRF) consensi compaction The TRF repeat consensi have been reduced to a compressed format. Long TRFs (>8) are represented by one consensus of the form n(N) where the "n" is the length of the consensus. Short TRFs (<=8) are represented by the alphabetical minimum of the rotation/revcomp set. Due to a small oversight in the compaction script, if the rot/rev/alphabetical minimum wasn't in the set of consensi in the first place, the consensus that represents the set is not the minimum but one of the existing consensi.   The mosquito database version has been updated to 2c, e.g. anopheles_gambiae_core_27_2c  Variation database   SNP data updated to dbSNP123 Schema changes in v27 Core database interpro table: unique restriction added affy_probe table: probeset column extended to varchar(40) external_db table: db_name is now varchar(27) density_feature table: added a index on seq_region_id Schema patch The 26 to 27 patch file is available in CVS at ensembl/sql/patch_26_27.sql to enable schema 26 databases to be patched to schema 27 without the need to re-download the data. . Variation database entirely new schema database replaces SNP and Lite databases New features in v27  LDView   LDView is a new display to present the linkage disequilibrium data in the new variation database. The LD values (both r2 and D') were calculated by a pairwise estimation for each population between SNPs genotyped in the same individuals and within a 100kb sliding window. The estimation used the established method of a maximum likelihood estimate of the proportion that each possible haplotype contributed to the double heterozygote.   LDView provides display of LD both graphically, using the standard "inverted triangle" style images, and as tabulated values. The LD values displayed can be selected as r2 or D', by population and across a zoomable window. LDView also provides a text export feature for easy downloading of the selected LD data.   LDView can be reached via links on SNPView, the SNP track on ContigView, and by the sitemap.   Currently LD data is only available for human but we anticipate more data in the future. We are hoping to improve the usefulness of our population genetics resources over 2005, and so would like to hear your opinion of LDView. Please send us your comments via the HelpDesk (helpdesk@ensembl.org).  SNPView   SNPView has been rewritten to use the new variation database and objects. It also presents an LD display for the default population, and provides links to LDView centred on the current SNP.  Image Exporting   To make it easier to export images from Ensembl, a new option has been added to the Export menu on ContigView, MultiContigView and GeneSNPView. If you check the boxes to "Include PDF links", "Include Postscript links", or "Include SVG links", then the appropriate links will appear beneath each image, allowing you to easily save the image in the required format.  Phenotypes GeneDAS   A new GeneDAS source, available for all species, presents phenotype data associated with the selected gene. The associations are either direct, through orthologues, or through protein families. The phenotype data are: C.elegans: Phenotypes originate from RNAi experiments, provided by the Sanger WormBase team(2004-09-17). Mouse: Phenotypes from "Mouse/Human Orthology with Phenotype Annotations" available from ftp://ftp.informatics.jax.org/pub/reports/index.html. (2004-11-04) Human: The OMIM morbid map from NCBI was used (2004-11-04) Zebrafish: Mutant data from ZFIN was used (2004-11-04) Fruitfly: Phenotype data provided by the FlyBase group at Department of Genetics, Cambridge University (2004-09-29).  GeneDAS by location   It is now possible to add a ContigView-style (location-based) DAS source as a GeneDAS source in GeneView, using the new "Ensembl Gene Location" mapping. This type of GeneDAS will list features that overlap the coordinates of the gene, making it straightforward to see if a DAS feature hits your gene of interest.  FeatureView   FeatureView has been extended to be able to show the locations of genes by any xref property of a gene, e.g. HUGO name, MIM ID, or Affy probe.